Control of Eukaryotic Genes

Control of Eukaryotic Genes

The BIG Questions… • How are genes turned on & off in eukaryotes? • How do cells with the same genes differentiate to perform completely different, specialized functions?

Evolution of gene regulation • Prokaryotes • single-celled • evolved to grow & divide rapidly • must respond quickly to changes in external environment • exploit transient resources • Gene regulation • turn genes on & off rapidly • flexibility & reversibility • adjust levels of enzymes for synthesis & digestion

Evolution of gene regulation • Eukaryotes • multicellular • evolved to maintain constant internal conditions while facing changing external conditions • homeostasis • regulate body as a whole • growth & development • long term processes • specialization • turn on & off large number of genes • must coordinate the body as a whole rather than serve the needs of individual cells

Collins I • List as many places that eukaryotic organisms regulate the expression of genes

Agenda • Continue notes • Still coming!! Operon activity

Points of control • The control of gene expression can occur at any step in the pathway from gene to functional protein 1. packing/unpacking DNA 2. transcription 3. mRNA processing 4. mRNA transport 5. translation 6. protein processing 7. protein degradation

1. DNA packing How do you fit all that DNA into nucleus? • DNA coiling & folding • double helix • nucleosomes • chromatin fiber • looped domains • chromosome from DNA double helix to condensed chromosome

8 histone molecules Nucleosomes • “Beads on a string” • 1st level of DNA packing • histone proteins • 8 protein molecules • positively charged amino acids • bind tightly to negatively charged DNA DNA packing movie

DNA packing as gene control • Degree of packing of DNA regulates transcription • tightly wrapped around histones • no transcription • genes turned off • heterochromatin darker DNA (H) = tightly packed • euchromatin lighter DNA (E) = loosely packed H E

DNA methylation • Methylation of DNA blocks transcription factors • no transcription  genes turned off • attachment of methyl groups (–CH3) to cytosine • C = cytosine • nearly permanent inactivation of genes • ex. inactivated mammalian X chromosome = Barr body

Histone acetylation • Acetylation of histones unwinds DNA • loosely wrapped around histones • enables transcription • genes turned on • attachment of acetyl groups (–COCH3) to histones • conformational change in histone proteins • transcription factors have easier access to genes

2. Transcription initiation • Control regions on DNA • promoter • nearby control sequence on DNA • binding of RNA polymerase & transcription factors • “base” rate of transcription • enhancer • distant control sequences on DNA • binding of activator proteins • “enhanced” rate (high level) of transcription

Model for Enhancer action • Enhancer DNA sequences • distant control sequences • Activator proteins • bind to enhancer sequence & stimulates transcription • Silencer proteins • bind to enhancer sequence & block gene transcription Turning on Gene movie

Transcription complex Activator Proteins • regulatory proteins bind to DNA at distant enhancer sites • increase the rate of transcription Enhancer Sites regulatory sites on DNA distant from gene Enhancer Activator Activator Activator Coactivator E F B RNA polymerase II H TFIID A Coding region T A T A Core promoter and initiation complex Initiation Complex at Promoter Site binding site of RNA polymerase

3. Post-transcriptional control • Alternative RNA splicing • variable processing of exons creates a family of proteins

4. Regulation of mRNA degradation • Life span of mRNA determines amount of protein synthesis • mRNA can last from hours to weeks RNA processing movie

NEW! RNA interference • Small interfering RNAs (siRNA) • short segments of RNA (21-28 bases) • bind to mRNA • create sections of double-stranded mRNA • “death” tag for mRNA • triggers degradation of mRNA • cause gene “silencing” • post-transcriptional control • turns off gene = no protein produced siRNA

Hot…Hotnew topicin biology Action of siRNA dicerenzyme mRNA for translation siRNA double-stranded miRNA + siRNA breakdownenzyme (RISC) mRNA degraded functionally turns gene off

1990s | 2006 RNA interference “for their discovery of RNA interference —gene silencing by double-stranded RNA” Andrew Fire Stanford Craig Mello U Mass

5. Control of translation • Block initiation of translation stage • regulatory proteins attach to 5' end of mRNA • prevent attachment of ribosomal subunits & initiator tRNA • block translation of mRNA to protein Control of translation movie

6-7. Protein processing & degradation • Protein processing • folding, cleaving, adding sugar groups, targeting for transport • Protein degradation • ubiquitin tagging • proteasome degradation Protein processing movie

1980s | 2004 Ubiquitin • “Death tag” • mark unwanted proteins with a label • 76 amino acid polypeptide, ubiquitin • labeled proteins are broken down rapidly in "waste disposers" • proteasomes Aaron Ciechanover Israel Avram Hershko Israel Irwin Rose UC Riverside

Proteasome • Protein-degrading “machine” • cell’s waste disposer • breaks down any proteins into 7-9 amino acid fragments • cellular recycling play Nobel animation

Gene Regulation 7 6 protein processing & degradation 1 & 2. transcription - DNA packing - transcription factors 3 & 4. post-transcription - mRNA processing - splicing - 5’ cap & poly-A tail - breakdown by siRNA 5. translation - block start of translation 6 & 7. post-translation - protein processing - protein degradation 5 4 initiation of translation mRNAprocessing 2 1 initiation of transcription mRNA protection 4 mRNA splicing 3

Turn yourQuestion Genes on!

Gene Regulation 7 6 1 & 2. _________________ - ____________________ - ____________________ 3 & 4. _________________ - ____________________ - ____________________ - ____________________ - ____________________ 5. _________________ - ____________________ ____________________ 6 & 7. _________________ - ____________________ - ____________________ 5 4 2 1 4 3

Control of Eukaryotic Genes